Re: Beowulf Cluster is very slow. Suggestions needed to increase the speed.

On 2014-10-21 09:42, suresh kannan wrote:
> Hello,
> 
>>>> Is the code running in the 'single system' the same running in
> parallel ?
> 
> If i install the software only in the head node (/usr/local/) mpirun
> says the software is not available in other nodes and the job
> terminates automatically. So, I have installed Gromacs (the software
> for simulation) only in head node (/home/mpiuser/)  and it
> automatically installed in all other nodes in /home/mpiuser/ (due to
> ssh without password, i guess so).

If you are using MPI, you can run the core in parallel within the same 
machine (1 process for each cpu core).
I think this is a god test to compare parallel running time with 
non-parallel because there isn't network involved.


>>>> Is the software using network efficiently ?
> 
> I have searched google but i am unable to find out. How can i find out
> that the software uses network efficiently. May be can I find that in
> openmpi manual?

Debugging...but if you don't write the code this is hard.


>>>> Why do you need a layer 3 ? Are cluster's nodes in different
> network ?
> 
> I learned from few documentations Master node must have two network
> cards for this type of cluster but we dont have in our systems. It
> seems from the discussions even the USB network card is slow. I dont
> know how to add additional network cards to the system. I am running
> clusters in the same network (only four systems using a single
> router).

You don't need a layer 3 switch (or a router) to connect head node with 
others nodes. A gigabit switch is enough.
Normally the head node have two network cards (A and B) because one (A) 
connect it with cluster's nodes and the other (B) connect the head node 
with users' network. So you access the head node by ip address of 
network card B and the ip address of network card A is used only for 
internal cluster communication. But this setup is not mandatory, is the 
one most used.


> It seems to me from the discussions that there are three problems
> 
> 1) we dont have two network cards systems.
No problem.


> 2) The router i was using (iptime 100Mbps). Although, the speed of
> those jobs increased still it is not efficient when i used 1000Mbps
> switch compare to a single system.
If possible, use gigabit switch with gigabit network cards.


> 3) I have used this tutorial
> http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-with-openmpi.html
> [2] (for gromacs) to install openmpi, gromacs. Only difference is i
> have used gcc compiler instead of intel compiler. That is the only
> difference (even they say gcc is make faster code than intel
> compilers) . I have read the config (log files for open mpi, gromacs,
> fftw libraries etc..) for errors but i found the installations of the
> softwares were quite ok. Even if i did some misconfiguration how do i
> find out that other than reading the config log files.  Is there are
> any other way?
I have never used this software, so I don't know. But if you can compile 
without errors with gcc it's ok. I personally prefer gcc because is open 
source.


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